A Quantitative Overview to Gene Expression Profiling in Animal Genetics

1
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
INTRODUCTION
Truths, Damn Truths Statistics in Gene
Expression Studies
Disclaimer
The Biologist and the Statistician are being
executed. They are both granted one last request.
The Statistician asks that he/she be allowed to
give one final lecture on his/her Grand Theory of
Statistics.
The Biologist asks that he/she be executed first.
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
2
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
THE RAW MATERIAL
This is a Cow
This is a Pig (female)
This is a Sheep
This is a Chicken
This is a Prawn
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
3
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY PROCESS
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
4
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY PROCESS
Definition of PROBE and TARGET
TARGET
PROBE
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
5
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY WET PROCESS
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
6
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY WET DRY PROCESSES
Experiment Design
RNA extraction Labeling Hybridization Scanning
Wet lab
Gridding Data transformation Normalization Stat
istical inference
Dry lab
Biological meaning
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
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A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY OUTPUT
What you see is what you get truly!
3 Spatial Features 1. Printing
block 2. Row 3. Column 2
Channels - Red - Foreground 4. Mean
5. Median 6. Std Dev -
Background 7. Mean 8. Median
9. Std Dev - Green - Foreground 10.
Mean 11. Median 12. Std Dev -
Background 13. Mean 14. Median 15.
Std Dev
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
8
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY APPLICATIONS

• Determine genes which are differentially
  expressed (DE).
• Connect DE genes to sequence databases to search
  for common upstream regions.
• Overlay DE genes on pathway diagrams.
• Relate expression levels to other information on
  cells, e.g. tumor types.
• Identify temporal and spatial trends in gene
  expression.
• Seek roles of genes based on patterns of
  co-regulation.
• Applications to Selective Breeding Schemes?

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
9
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
MICROARRAY PROCESS

1. Biologists dont care 10
2. Statisticians are bad . 20
3. Unrealistic expectations 70

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
10
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
CHALLENGES
Time Dependent
Data Dependent
Human Dependent
Chronology
Paradigm
Skill Integration
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
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A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Historical

• Traditionally Statistics grew alongside
  Agriculture
• Introduction to Statistical Analysis

• Law of Large Numbers
• Central Limit Theorem

SST SSM SSE

• Pythagoras Theorem

• Nowadays Statistics alongside (Bio)Technology

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
12
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Excitement (source of)
Eg. Always log spot intensities and ratios T
Speed. Hints and Prejudices

• Biochemist My software does it, therefore its
  great!

• Statistician Well, I need further evidence to be
  convinced

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
13
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Balance

• Too many Statisticians

Evidence It takes 1 ship, 10 days to cross the
ocean Question How many days does it take for 10
ships to cross the ocean?
Evidence It takes 1 builder, 10 days to build a
wall Question How many days does it take for 10
builders to build a wall?
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
14
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Balance

• Too many Statisticians

PHD SCHOLARSHIP Statistical Science
Program MATHEMATICAL SCIENCES INSTITUTE THE
AUSTRALIAN NATIONAL UNIVERSITY Stipend 22,771
(2002 rate, indexed annually, tax free) A PhD
Scholarship (APAI) is being offered by the
Mathematical Sciences Institute at The ANU. An
ARC Linkage Grant held by Professors Peter Hall
(ANU) and Don Poskitt (Monash University), in
conjunction with BAE Systems, Melbourne, will
fund the scholarship. The research problem is in
the area of stochastic control applied to ship
motion, and involves the development and
implementation of both parametric and
nonparametric methods. The successful applicant
will have a strong interest in statistical
methodology, computational techniques,
theoretical analysis, and the development of
statistical research problems.
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
15
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Balance

• Too many Biochemists

Treated?
No
Yes
100
150
No
Died?
Yes
120
120
Survival Rates Treated 150/270
55.55 Non-Tr 100/220 45.45
22 Increase!
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
16
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Balance

• Too many Biochemists

r 0.87
y




r 0.00


















r 0.00










x
Armidale Animal Breeding Summer Course, UNE, Feb.
2006
17
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Interdisciplinary Skills
Minimal knowledge of the application discipline
is needed
However, simply keeping track of the literature
is an enormous task.

1. Animal Science
2. Journal of Animal Science
3. Journal of Dairy Science
4. Genetic Selection Evolution
5. Livestock Production Science
6. a couple or so more.

1. NPG Nature, Nature Genetics, Nature Review
   Genetics, Nature Biotechnology, Nature Methods,
   Nature Computational Biology.
2. BMC Bioinformatics, Genomics.
3. Science
4. Genome Research
5. Bioinformatics
6. PNAS
7. Mammalian Genome
8. Nucleic Acids Reseach
9. and many many more.

1. JASA
2. JABES
3. Biostatistics

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
18
A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Challenges
Human Dependent
Interdisciplinary Skills
Minimal knowledge of the application discipline
is needed
Failing that, the Statisticians will win,
..but with the wrong weapons.

1. Amount of Expression Amount of Response
2. Same cut-off point to judge all genes
3. Over-emphasis in normalization (Thus, reject
   Boutique Arrays)
4. Over-emphasis in variance stabilization

Armidale Animal Breeding Summer Course, UNE, Feb.
2006
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A Quantitative Overview to Gene Expression
Profiling in Animal Genetics
Information Amount vs Quality
Probability (certainty) of both Female?
Case 1. No Information
1/4
Case 2. The one on the left is female
1/2
Case 3. One of them is female
.1/3
Armidale Animal Breeding Summer Course, UNE, Feb.
2006